Sun Kim

CAREPath improves drug repurposing by combining semantic path embeddings with mechanism-context augmentation in biomedical knowledge graphs, achieving better performance than existing methods.

This study introduces a context-aware hierarchical fusion model for drug relational learning, showing improved performance in predicting drug-drug interactions and side effects across different contexts.

The paper evaluates and optimizes sequence-based gene regulatory deep learning models using a DREAM Challenge dataset, showing improvements through architectural and training strategy refinements.

EnsDTI improves drug-target interaction prediction by combining multiple models and providing confidence scores, achieving a 2.7% accuracy improvement over baselines.

This study shows HIV-1 integrates near R-loops in the host genome, linking viral integration to R-loop formation and suggesting new therapeutic strategies.

The paper identifies mechanisms by which CRISPR, base editors, and prime editors cause large DNA deletions and proposes strategies to mitigate them.

This paper develops a method to predict cancer patient survival using 3D genome-aware features derived from DNA methylation data, showing improved accuracy across seven cancer types.

Metheor calculates DNA methylation heterogeneity from bisulfite reads, offering faster and more efficient analysis than existing tools.

EnsDTI-kinase is a web-server that combines eight computational models to predict kinase-inhibitor interactions, offering improved accuracy and mutagenesis analysis.

This paper introduces a multi-layer guilt-by-association approach for drug repurposing by integrating clinical knowledge into biological networks, improving drug-disease association prediction accuracy.

This paper introduces Chromoformer, a transformer-based model that improves the quantitative analysis of histone codes in gene regulation by incorporating 3D chromatin interactions.

This study identifies conserved gene regulatory networks in the root cambium of radish and Arabidopsis that link environmental sensing to growth, highlighting ERF-1 as a key regulator.

The paper uses a logic-based approach to analyze gene expression differences in breast cancer subtypes, identifying pathway crosstalk between TNF, TGFB1, and EGF in basal-like breast cancer.